Bulk segregant RNA-seq reveals expression and positional candidate genes and allele-specific expression for disease resistance against enteric septicemia of catfish

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Wang, Ruijia ^a   Sun, Luyang ^a   Bao, Lisui ^a   Zhang, Jiaren ^a   Jiang, Yanliang ^a   Yao, Jun ^a   Song, Lin ^a   Feng, Jianbin ^a   Liu, Shikai ^a   Liu, Zhanjiang ^a  

^a AUBURN UNIVERSITY   (United States)

Author keywords

Allele specific expression; Bulk segregant analysis; Catfish; Disease resistance; RNA seq

Indexed keywords

ALLELE; ANIMAL EXPERIMENT; ARTICLE; BULKED SEGREGANT ANALYSIS; CONTROLLED STUDY; DISEASE RESISTANCE; EDWARDSIELLA ICTALURI; ENTERIC SEPTICEMIA OF CATFISH; GENE EXPRESSION; GENE IDENTIFICATION; GENE MAPPING; GENE SEGREGATION; NONHUMAN; PHENOTYPE; RNA ISOLATION; RNA SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; CATFISHES; DISEASE RESISTANCE; EDWARDSIELLA ICTALURI; ENTEROBACTERIACEAE INFECTIONS; FISH DISEASES; GENE EXPRESSION PROFILING; POLYMORPHISM, SINGLE NUCLEOTIDE; SEPSIS; SEQUENCE ANALYSIS, RNA;

EID: 84891363864     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-929     Document Type: Article

References (63)

1. Oleksiak MF, Roach JL, Crawford DL. Natural variation in cardiac metabolism and gene expression in Fundulus heteroclitus. Nat Genet 2004, 37:67-72. 1447534, 15568023.
2. Hallman D, Boerwinkle E, Saha N, Sandholzer C, Menzel H, Csazar A, Utermann G. The apolipoprotein E polymorphism: a comparison of allele frequencies and effects in nine populations. Am J Hum Genet 1991, 49:338. 1683282, 1867194.
3. He G, Chen B, Wang X, Li X, Li J, He H, Yang M, Lu L, Qi Y, Wang X. Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids. Genome Biol 2013, 14:R57. 10.1186/gb-2013-14-6-r57, 3707063, 23758703.
4. Bevan M, Uauy C. Genomics reveals new landscapes for crop improvement. Genome Biol 2013, 14:206. 10.1186/gb-2013-14-6-206, 23796126.
5. Young N. QTL mapping and quantitative disease resistance in plants. Annu Rev Phytopathol 1996, 34:479-501. 10.1146/annurev.phyto.34.1.479, 15012553.
6. Bunney WE, Bunney BG, Vawter MP, Tomita H, Li J, Evans SJ, Choudary PV, Myers RM, Jones EG, Watson SJ. Microarray technology: a review of new strategies to discover candidate vulnerability genes in psychiatric disorders. Am J Psychiatry 2003, 160:657-666. 10.1176/appi.ajp.160.4.657, 12668351.
7. Wang Z, Gerstein M, Snyder M. RNA-seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10:57-63. 10.1038/nrg2484, 2949280, 19015660.
8. Oshlack A, Robinson MD, Young MD. From RNA-seq reads to differential expression results. Genome Biol 2010, 11:220. 10.1186/gb-2010-11-12-220, 3046478, 21176179.
9. Molinié B, Georgel P. Genetic and epigenetic regulations of prostate cancer by genistein. Drug News Perspect 2009, 22:247-254. 10.1358/dnp.2009.22.5.1378633, 19609462.
10. Ng J-H, Heng J-CD, Loh Y-H, Ng H-H. Transcriptional and epigenetic regulations of embryonic stem cells. Mutat Res 2008, 647:52-58. 10.1016/j.mrfmmm.2008.08.009, 18778721.
11. He H, Hua X, Yan J. Epigenetic regulations in hematopoietic Hox code. Oncogene 2010, 30:379-388.
12. Gururani MA, Venkatesh J, Upadhyaya CP, Nookaraju A, Pandey SK, Park SW. Plant disease resistance genes: current status and future directions. Physiol Mol Plant Pathol 2012, 78:51-65.
13. Zhao S, Zhu M, Chen H. Immunogenomics for identification of disease resistance genes in pigs: a review focusing on Gram-negative bacilli. J Anim Sci 2012, 3:1-13.
14. Guangli S, Zhanjing H, Congfen H, Yinzhu S, Wang J. Identification of the molecular markers linked to the salt-resistance locus in the wheat using RAPD-BSA technique. Acta Bot Sin 2001, 43:598.
15. Cheema KK, Grewal NK, Vikal Y, Sharma R, Lore JS, Das A, Bhatia D, Mahajan R, Gupta V, Bharaj TS. A novel bacterial blight resistance gene from Oryza nivara mapped to 38 kb region on chromosome 4 L and transferred to Oryza sativa L. Genet Res 2008, 90:397.
16. Dussle C, Quint M, Melchinger A, Xu M, Lübberstedt T. Saturation of two chromosome regions conferring resistance to SCMV with SSR and AFLP markers by targeted BSA. Theor Appl Genet 2003, 106:485-493.
17. Asnaghi C, Roques D, Ruffel S, Kaye C, Hoarau J-Y, Telismart H, Girard J, Raboin L, Risterucci A, Grivet L. Targeted mapping of a sugarcane rust resistance gene (Bru1) using bulked segregant analysis and AFLP markers. Theor Appl Genet 2004, 108:759-764. 10.1007/s00122-003-1487-6, 14586507.
18. Becker A, Chao D-Y, Zhang X, Salt DE, Baxter I. Bulk segregant analysis using single nucleotide polymorphism microarrays. PLoS One 2011, 6:e15993. 10.1371/journal.pone.0015993, 3029305, 21297997.
19. Lee BY, Penman D, Kocher T. Identification of a sex-determining region in Nile tilapia (Oreochromis niloticus) using bulked segregant analysis. Anim Genet 2003, 34:379-383. 10.1046/j.1365-2052.2003.01035.x, 14510676.
20. Ruyter-Spira CP, Gu Z, Van der Poel J, Groenen M. Bulked segregant analysis using microsatellites: mapping of the dominant white locus in the chicken. Poult Sci 1997, 76:386-391.
21. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 2008, 3:e3376. 10.1371/journal.pone.0003376, 2557064, 18852878.
22. Wenger JW, Schwartz K, Sherlock G. Bulk segregant analysis by high-throughput sequencing reveals a novel xylose utilization gene from Saccharomyces cerevisiae. PLoS Genet 2010, 6:e1000942. 10.1371/journal.pgen.1000942, 2869308, 20485559.
23. Ayers KL, Davidson NM, Demiyah D, Roeszler KN, Grutzner F, Sinclair AH, Oshlack A, Smith CA. RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken embryos and allows comprehensive annotation of W-chromosome genes. Genome Biol 2013, 14:R26. 10.1186/gb-2013-14-3-r26, 23531366.
24. Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 2008, 5:613-619. 10.1038/nmeth.1223, 18516046.
25. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008, 18:1509-1517. 10.1101/gr.079558.108, 2527709, 18550803.
26. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Methods 2008, 5:621-628. 10.1038/nmeth.1226, 18516045.
27. Pepke S, Wold B, Mortazavi A. Computation for ChIP-seq and RNA-seq studies. Nat Methods 2009, 6:S22-S32. 10.1038/nmeth.1371, 19844228.
28. Trick M, Adamski NM, Mugford SG, Jiang C-C, Febrer M, Uauy C. Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat. BMC Plant Biol 2012, 12:14. 10.1186/1471-2229-12-14, 3296661, 22280551.
29. Liu S, Yeh C-T, Tang HM, Nettleton D, Schnable PS. Gene mapping via bulked segregant RNA-seq (BSR-Seq). PLoS ONE 2012, 7:e36406. 10.1371/journal.pone.0036406, 3346754, 22586469.
30. Chatakondi N, Yant D, Dunham R. Commercial production and performance evaluation of channel catfish, Ictalurus punctatus female× blue catfish, Ictalurus furcatus male F-1 hybrids. Aquaculture 2005, 247:8.
31. Liu Z, Karsi A, Li P, Cao D, Dunham R. An AFLP-based genetic linkage map of channel catfish (Ictalurus punctatus) constructed by using an interspecific hybrid resource family. Genetics 2003, 165:687-694. 1462775, 14573480.
32. Kucuktas H, Wang S, Li P, He C, Xu P, Sha Z, Liu H, Jiang Y, Baoprasertkul P, Somridhivej B. Construction of genetic linkage maps and comparative genome analysis of catfish using gene-associated markers. Genetics 2009, 181:1649-1660. 10.1534/genetics.108.098855, 2666527, 19171943.
33. Ninwichian P, Peatman E, Liu H, Kucuktas H, Somridhivej B, Liu S, Li P, Jiang Y, Sha Z, Kaltenboeck L. Second-generation genetic linkage map of catfish and its integration with the BAC-based physical map. G3 2012, 2:1233-1241. 2012, 3464116, 23050234.
34. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome research 2012, 22:568-576. 10.1101/gr.129684.111, 3290792, 22300766.
35. Michelmore RW, Paran I, Kesseli R. Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci 1991, 88:9828-9832. 10.1073/pnas.88.21.9828, 52814, 1682921.
36. Peatman E, Baoprasertkul P, Terhune J, Xu P, Nandi S, Kucuktas H, Li P, Wang S, Somridhivej B, Dunham R. Expression analysis of the acute phase response in channel catfish (Ictalurus punctatus) after infection with a Gram-negative bacterium. Dev Comp Immunol 2007, 31:1183-1196. 10.1016/j.dci.2007.03.003, 17449095.
37. Peatman E, Terhune J, Baoprasertkul P, Xu P, Nandi S, Wang S, Somridhivej B, Kucuktas H, Li P, Dunham R. Microarray analysis of gene expression in the blue catfish liver reveals early activation of the MHC class I pathway after infection with Edwardsiella ictaluri. Mol Immunol 2008, 45:553-566. 10.1016/j.molimm.2007.05.012, 17599411.
38. Li C, Zhang Y, Wang R, Lu J, Nandi S, Mohanty S, Terhune J, Liu Z, Peatman E. RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus. Fish Shellfish Immunol 2012, 32:816-827. 10.1016/j.fsi.2012.02.004, 22366064.
39. Sigel S, Bunk S, Meergans T, Doninger B, Stich K, Stulnig T, Derfler K, Hoffmann J, Deininger S, von Aulock S. Apolipoprotein B100 is a suppressor of Staphylococcus aureus-induced innate immune responses in humans and mice. Eur J Immunol 2012, 42:2983-2989. 10.1002/eji.201242564, 22806614.
40. Kesavalu L, Lucas A, Verma R, Liu L, Dai E, Sampson E, Progulske-Fox A. Increased atherogenesis during Streptococcus mutans infection in ApoE-null mice. Dent Res J 2012, 91:255-260.
41. Peterson MM, Mack JL, Hall PR, Alsup AA, Alexander SM, Sully EK, Sawires YS, Cheung AL, Otto M, Gresham HD. Apolipoprotein B is an innate barrier against invasive Staphylococcus aureus infection. Cell Host Microbe 2008, 4:555-566. 10.1016/j.chom.2008.10.001, 2639768, 19064256.
42. Morgan RW, Sofer L, Anderson AS, Bernberg EL, Cui J, Burnside J. Induction of host gene expression following infection of chicken embryo fibroblasts with oncogenic Marek's disease virus. J Virol 2001, 75:533-539. 10.1128/JVI.75.1.533-539.2001, 113947, 11119623.
43. Wozniak MA, Shipley SJ, Dobson CB, Parker SP, Scott FT, Leedham-Green M, Breuer J, Itzhaki RF. Does apolipoprotein E determine outcome of infection by varicella zoster virus and by Epstein Barr virus?. Eur J Hum Genet 2007, 15:672-678. 10.1038/sj.ejhg.5201812, 17356546.
44. Shifman S, Kuypers J, Kokoris M, Yakir B, Darvasi A. Linkage disequilibrium patterns of the human genome across populations. Hum Mol Genet 2003, 12:771-776. 10.1093/hmg/ddg088, 12651872.
45. Buckland PR. Allele-specific gene expression differences in humans. Hum Mol Genet 2004, 13:R255-R260. 10.1093/hmg/ddh227, 15358732.
46. Bell CG, Beck S. Advances in the identification and analysis of allele-specific expression. Genome Med 2009, 1:56. 10.1186/gm56, 2689448, 19490587.
47. Wray GA. The evolutionary significance of cis-regulatory mutations. Nat Rev Genet 2007, 8:206-216. 10.1038/nrg2063, 17304246.
48. Milani L, Lundmark A, Nordlund J, Kiialainen A, Flaegstad T, Jonmundsson G, Kanerva J, Schmiegelow K, Gunderson KL, Lönnerholm G. Allele-specific gene expression patterns in primary leukemic cells reveal regulation of gene expression by CpG site methylation. Genome Res 2009, 19:1-11. 2612957, 18997001.
49. Petronis A. The genes for major psychosis: aberrant sequence or regulation?. Neuropsychopharmacology 2000, 23:1-12. 10.1016/S0893-133X(00)00127-5, 10869881.
50. Morgan HD, Sutherland HG, Martin DI, Whitelaw E. Epigenetic inheritance at the agouti locus in the mouse. Nat Genet 1999, 23:314-318. 10.1038/15490, 10545949.
51. Kato MV, Shimizu T, Nagayoshi M, Kaneko A, Sasaki MS, Ikawa Y. Genomic imprinting of the human serotonin-receptor (HTR2) gene involved in development of retinoblastoma. Am J Hum Genet 1996, 59:1084. 1914818, 8900237.
52. Koivisto U-M, Palvimo JJ, Jänne OA, Kontula K. A single-base substitution in the proximal Sp1 site of the human low density lipoprotein receptor promoter as a cause of heterozygous familial hypercholesterolemia. Proc Natl Acad Sci 1994, 91:10526-10530. 10.1073/pnas.91.22.10526, 45054, 7937987.
53. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol 2011, 29:644-652. 10.1038/nbt.1883, 3571712, 21572440.
54. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659. 10.1093/bioinformatics/btl158, 16731699.
55. Huang X, Madan A. CAP3: a DNA sequence assembly program. Genome Res 1999, 9:868-877. 10.1101/gr.9.9.868, 310812, 10508846.
56. Brockman W, Alvarez P, Young S, Garber M, Giannoukos G, Lee WL, Russ C, Lander ES, Nusbaum C, Jaffe DB. Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res 2008, 18:763-770. 10.1101/gr.070227.107, 2336812, 18212088.
57. Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 2010, 11:R25. 10.1186/gb-2010-11-3-r25, 2864565, 20196867.
58. Kal AJ, van Zonneveld AJ, Benes V, van den Berg M, Koerkamp MG, Albermann K, Strack N, Ruijter JM, Richter A, Dujon B. Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources. Mol Biol Cell 1999, 10:1859-1872. 10.1091/mbc.10.6.1859, 25383, 10359602.
59. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Stat Methodol 1995, 57:289-300.
60. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25:2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943.
61. Kofler R, Pandey RV, Schlötterer C. PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). Bioinformatics 2011, 27:3435-3436. 10.1093/bioinformatics/btr589, 3232374, 22025480.
62. Fisher RA. On the interpretation of χ 2 from contingency tables, and the calculation of P. J R Stat Soc 1922, 85:87-94.
63. Liu S, Zhou Z, Lu J, Sun F, Wang S, Liu H, Jiang Y, Kucuktas H, Kaltenboeck L, Peatman E. Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array. BMC Genomics 2011, 12:53. 10.1186/1471-2164-12-53, 3033819, 21255432.